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Using neural networks for reducing the dimensions of single-cell RNA-Seq data
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Abstract
While only recently developed, the ability to profile expression data in single cells (scRNA-Seq) has already led to several important studies and findings. However, this technology has also raised several new computational challenges. These include questions about the best methods for clustering scRNA-Seq data, how to identify unique group of cells in such experiments, and how to determine the state or function of specific cells based on their expression profile. To address these issues we develop and test a method based on neural networks (NN) for the analysis and retrieval of single cell RNA-Seq data. We tested various NN architectures, some of which incorporate prior biological knowledge, and used these to obtain a reduced dimension representation of the single cell expression data. We show that the NN method improves upon prior methods in both, the ability to correctly group cells in experiments not used in the training and the ability to correctly infer cell type or state by querying a database of tens of thousands of single cell profiles. Such database queries (which can be performed using our web server) will enable researchers to better characterize cells when analyzing heterogeneous scRNA-Seq samples.
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“This idea was recently explored by Lin et al. (2017), who predicted cell type and state using a deep neural network for which the structure was determined based on the hierarchical organization of transcriptional regulatory factors in the nucleus.”
From Visible Machine Learning for Biomedicine (2018) · cites this paper as Lin et al., 2017
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“In contrast, direct incorporation of the biological structure of cells and tissues, such as explored by Lin et al. (2017) and Ma et al. (2018), leads to a ready-made working model of how biological inputs, such as genotype, are compressed to determine outcomes.”
From Visible Machine Learning for Biomedicine (2018) · cites this paper as Lin et al., 2017
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MethodPezoulas, V. C., Hazapis, O. G., Lаgopati, N., Exarchos, T. P., Goules, A. V., Tzioufas, A. G., Fotiadis, D. I., Stratis, I. G., Yannacopoulos, A. N., & Gorgoulis, V. G. (2021) · Cancer Genomics & Proteomics · doi:10.21873/cgp.20284 · Cited by 29
Performance Evaluation of ANOVA and RFE Algorithms for Classifying Microarray Dataset Using SVM
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“[74]; the link to their retrieval method is http:// sb.”
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A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data
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Pathogenic gene prediction based on network embedding
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“As shown by the calculated adjusted random index (ARI) [11, 12], choice of insulating parameter did influence the identified modules, but the modular composition remained generally robust (Supplementary Fig.”
BackgroundVisible neural networks for multi-omics integration: a critical review
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AutoGenome: An AutoML tool for genomic research
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“Furthermore, the noise-filtering capabilities of the model, derived from both the topology and the sparsity-inducing priors used, can help with the visualizations [23, 51].”
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BackgroundSingle cell RNA-sequencing: replicability of cell types
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The progressive application of single-cell RNA sequencing technology in cardiovascular diseases
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Metadata
- Authors
- Lin, C., Jain, S., Kim, H., & Bar-Joseph, Z.
- Affiliations
- Carnegie Mellon University (US)
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07-31
- Volume
- 45
- Issue
- 17
- Pages
- e156-e156
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5737331
- OpenAlex
- W2741564801
- Semantic Scholar
- c4d33e602615608d29bb296591591fe4e51b7bf2
- Cited by
- 197
- References
- 65
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 15 · 2023: 14 · 2022: 21 · 2021: 31 · 2020: 43 · 2019: 37 · 2018: 23 · 2017: 1
- FWCI
- 11.62
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1356505)
- National Institutes of Health
- National Heart, Lung, and Blood Institute (U01HL122626)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- single-cell RNA sequencing, dimensionality reduction, artificial neural networks, cell clustering, cell type annotation, heterogeneous cell populations, web server
- MeSH terms
- Gene Expression Regulation, Humans, RNA, Software, Cluster Analysis, Neural Networks, Computer, Sequence Analysis, RNA, Computational Biology, Gene Expression Profiling, Protein Interaction Mapping, Databases, Genetic, Multifactor Dimensionality Reduction, Single-Cell Analysis, Datasets as Topic
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